can you try to disable all plugins? Maybe one causes a conflict. Kriesi released an update some weeks ago which fixes some bugs with the AviaSlider and IE9. I could only see one control bar under the slider.

Sorry I didn’t reply earlier – I managed to find the problem. I had moved some <script> links out of the wp_head and placed them after wp_head was called so I guess they replaced what was called previously and thus broke the JS.